Package org.biojava.bio.seq.db

Class AnnotatedSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

org.biojava.bio.seq.db.AnnotatedSequenceDB

All Implemented Interfaces:

Serializable, SequenceDB, SequenceDBLite, Changeable

public class AnnotatedSequenceDB
extends AbstractSequenceDB
implements SequenceDB, Serializable

SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
AnnotatedSequenceDB(SequenceDB parent, SequenceAnnotator a)

Method Summary

Modifier and Type	Method	Description
protected Sequence	doAnnotation(Sequence seq)	Apply the annotation to a sequence.
String	getName()	Get the name of this sequence database.
SequenceDB	getParent()	Get the original sequenceDB from this annotated sequenceDB.
Sequence	getSequence(String id)	Retrieve a single sequence by its id.
Set	ids()	Get an immutable set of all of the IDs in the database.
SequenceIterator	sequenceIterator()	Returns a SequenceIterator over all sequences in the database.

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB

addSequence, filter, removeSequence

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.db.SequenceDB

filter

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite

addSequence, removeSequence

Constructor Detail

AnnotatedSequenceDB

public AnnotatedSequenceDB(SequenceDB parent,
                           SequenceAnnotator a)

Method Detail

getParent

public SequenceDB getParent()

Get the original sequenceDB from this annotated sequenceDB.

getName

public String getName()

Description copied from interface: SequenceDBLite

Get the name of this sequence database.

Specified by:

getName in interface SequenceDBLite

Returns:

the name of the sequence database, which may be null.

getSequence

public Sequence getSequence(String id)
                     throws BioException

Description copied from interface: SequenceDBLite

Retrieve a single sequence by its id.

Specified by:

getSequence in interface SequenceDBLite

Parameters:

id - the id to retrieve by

Returns:

the Sequence with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException - if there was a failure in retrieving the sequence

ids

public Set ids()

Description copied from interface: SequenceDB

Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

Specified by:

ids in interface SequenceDB

Returns:

a Set of ids - at the moment, strings

sequenceIterator

public SequenceIterator sequenceIterator()

Description copied from interface: SequenceDB

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.

Specified by:

sequenceIterator in interface SequenceDB

Overrides:

sequenceIterator in class AbstractSequenceDB

Returns:

a SequenceIterator over all sequences

doAnnotation

protected Sequence doAnnotation(Sequence seq)
                         throws BioException

Apply the annotation to a sequence.

Parameters:

seq - the sequence to annotate.

Throws:

BioException